Lo-Fi Games

As it is now the only ways to improve them are to deliver bounties to the office (that im aware of) but that isnt plausible when you have negative relations with a faction. There should be ways to improve relations whilst not being attacked etc in the process eg trading in general with them (some sort of truce system needs to be established) killing mobs that are near the city as a quest, gifts etc.

Good idea.

But, there's is currently couple more sure ways to improve faction relationship that i know of: healing faction members after battle and also through certain dialogues, like one with Moll about joining Flotsam Ninjas. I have no idea how many more of such dialogues there is, however.

There are supposed to be several faction relation things added not sure what they will be.
Till then you can look up the diplomat mods. there are several. these add diplomat characters who allow you to buy back good relations for a price.

this is currently being worked on
hence why we recently got the ability to join the ninjas and Holy nation and now from what i hear, United Cities as well down south.

More options are being added, just takes time.